5A3U

HIF prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H- 1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain.

Chan, M.C.Atasoylu, O.Hodson, E.Tumber, A.Leung, I.K.H.Chowdhury, R.Gomez-Perez, V.Demetriades, M.Rydzik, A.M.Holt-Martyn, J.Tian, Y.Bishop, T.Claridge, T.D.W.Kawamura, A.Pugh, C.W.Ratcliffe, P.J.Schofield, C.J.

(2015) PLoS One 10: 32004

  • DOI: 10.1371/journal.pone.0132004
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human ...

    As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.


    Related Citations: 
    • Selective Small Molecule Probes for the Hypoxia Inducible Factor (Hif) Prolyl Hydroxylases.
      Chowdhury, R., Candela-Lena, J.I., Chan, M.C., Greenald, D.J., Yeoh, K.K., Tian, Y., Mcdonough, M.A., Tumber, A., Rose, N.R., Conejo-Garcia, A., Demetriades, M., Mathavan, S., Kawamura, A., Lee, M.K., Van Eeden, F., Pugh, C.W., Ratcliffe, P.J., Schofield, C.J.
      (2013) ACS Chem Biol 8: 1488

    Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EGL NINE HOMOLOG 1A, B, C252Homo sapiensMutation(s): 0 
Gene Names: EGLN1C1orf12PNAS-118PNAS-137
EC: 1.14.11.2 (PDB Primary Data), 1.14.11.29 (PDB Primary Data), 1.14.11 (PDB Primary Data)
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R8J
Query on R8J

Download CCD File 
A, B, C
6-(5-oxo-4-(1H-1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid
C11 H8 N6 O3
MRJSXXCYZJCFSP-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.192 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.939α = 90
b = 154.939β = 90
c = 85.401γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation